SAXSdb — 3ygs

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1. Protein Identity and Related Structures Protein Identity & Related Structures

APOPTOTIC PROTEASE ACTIVATING FACTOR 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–95	Fragment：CASPASE RECRUITMENT DOMAIN (CARD)	PROCASPASE 9 × 1 （P55211）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.50 Å R-free 0.299

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3YGS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C15 SOLUTION STRUCTURE OF APAF-1 CARD Deposited 1999-07-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–97（97 aa） Fragment：CASPASE RECRUITMENT DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 1；Pressure AMBIENT NMR sample composition 1MM 15N LABELED APAF-1 CARD, 20 MM PHOSPHATE BUFFER, 50 MM NACL NMR sample composition 1MM 13C LABELED APAF-1 CARD, 20 MM PHOSPHATE BUFFER, 50 MM NACL NMR sample composition 1MM NON-LABELED APAF-1 CARD, 20 MM PHOSPHATE BUFFER, 50 MM NACL NMR sample composition 1MM 13C,15N LABELED, 80%DEUTERATED APAF-1 CARD, 20 MM PHOSPHATE BUFFER, 50 MM NACL	Resolution not provided
1CWW SOLUTION STRUCTURE OF THE CASPASE RECRUITMENT DOMAIN (CARD) FROM APAF-1 Deposited 1999-08-26	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–97（97 aa） Fragment：CASPASE RECRUITMENT DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；30 K NMR measurement conditions pH 6.7；30 K NMR measurement conditions pH 6.7；30 K NMR sample composition UNLABELLED 1.5MM APAF-1 CARD 20MM SODIUM PHOSPHATE PH 6.7 75MM NACL 2MM DITHIOTHREITOL NMR sample composition U-15N 1.5MM APAF-1 CARD 20MM SODIUM PHOSPHATE PH 6.7 75MM NACL 2MM DITHIOTHREITOL NMR sample composition U-15N; U-13C 1.5MM APAF-1 CARD 20MM SODIUM PHOSPHATE PH 6.7 75MM NACL 2MM DITHIOTHREITOL	Resolution not provided
1CY5 CRYSTAL STRUCTURE OF THE APAF-1 CARD Deposited 1999-08-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–97（97 aa） Fragment：CASPASE RECRUITMENT DOMAIN	Not recorded	ZN ZINC ION × 5 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；HANGING DROP VAPOR DIFFUSION WITH EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTIONS. PROTEIN SOLUTION: 5-20 MG/ML PROTEIN IN 0.02 MOLAR TRIS (PH 8.0-8.5) , 0.1-0.2 MOLAR SODIUM CHLORIDE. 0.005 MOLAR 2-MERCAPTOETHANOL RESERVOIR SOLUTION: 8-20% (W/V) PEG 8000, 0.2 MOLAR TRIS (PH 7.5-8.0), 0.05-0.2 MOLAR ZINC ACETATE., VAPOR DIFFUSION, HANGING DROP, temperature 17K	Resolution 1.30 Å R-free 0.199
1Z6T Structure of the apoptotic protease-activating factor 1 bound to ADP Deposited 2005-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–591（591 aa） Fragment：Apaf-1, residues 1-591	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；276 K；HEPES, ammonium acetate, PEG-3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 276K, pH 7.10	Resolution 2.21 Å R-free 0.244
1Z6T Structure of the apoptotic protease-activating factor 1 bound to ADP Deposited 2005-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–591（591 aa） Fragment：Apaf-1, residues 1-591	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；276 K；HEPES, ammonium acetate, PEG-3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 276K, pH 7.10	Resolution 2.21 Å R-free 0.244
1Z6T Structure of the apoptotic protease-activating factor 1 bound to ADP Deposited 2005-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–591（591 aa） Fragment：Apaf-1, residues 1-591	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；276 K；HEPES, ammonium acetate, PEG-3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 276K, pH 7.10	Resolution 2.21 Å R-free 0.244
1Z6T Structure of the apoptotic protease-activating factor 1 bound to ADP Deposited 2005-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–591（591 aa） Fragment：Apaf-1, residues 1-591	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；276 K；HEPES, ammonium acetate, PEG-3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 276K, pH 7.10	Resolution 2.21 Å R-free 0.244
2P1H Rapid Folding and Unfolding of Apaf-1 CARD Deposited 2007-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–92（92 aa） Fragment：CARD domain (Residues 1-92)	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；200 mM Tris-HCl, pH 6.1, 200 mM zinc acetate, 17% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.59 Å R-free 0.297
2YGS CARD DOMAIN FROM APAF-1 Deposited 1999-05-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–92（92 aa） Fragment：CASPASE RECRUITMENT DOMAIN (CARD)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 1.60 Å R-free 0.236
3J2T An improved model of the human apoptosome Deposited 2012-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–1248（1248 aa） Chain B 1–1248（1248 aa） Chain C 1–1248（1248 aa） Chain D 1–1248（1248 aa） Chain E 1–1248（1248 aa） Chain F 1–1248（1248 aa） Chain G 1–1248（1248 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 7	ELECTRON MICROSCOPY cryo-EM buffer low salt HEPES buffer；pH 7.5；20mM HEPES, 10mM KCl, 1.5mM MgCl2, 1mM EDTA, 1mM EGTA, 1mM DTT cryo-EM vitrification conditions Blot for 2 seconds before plunging；77 K；Cryogen ETHANE；Blot for 2 seconds before plunging (FEI VITROBOT MARK III)	Resolution 9.50 Å
3JBT Atomic structure of the Apaf-1 apoptosome Deposited 2015-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–1248（1248 aa） Chain C 1–1248（1248 aa） Chain E 1–1248（1248 aa） Chain G 1–1248（1248 aa） Chain I 1–1248（1248 aa） Chain K 1–1248（1248 aa） Chain M 1–1248（1248 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 7	ELECTRON MICROSCOPY cryo-EM buffer 20 mM HEPES (pH 7.5), 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM DTT；pH 7.5；20 mM HEPES (pH 7.5), 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM DTT cryo-EM vitrification conditions Blot for 2.5 seconds before plunging；Cryogen ETHANE	Resolution 3.80 Å
4RHW Crystal structure of Apaf-1 CARD and caspase-9 CARD complex Deposited 2014-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–97（97 aa） Fragment：card domain Chain B 1–97（97 aa） Fragment：card domain Chain C 1–97（97 aa） Fragment：card domain Chain D 1–97（97 aa） Fragment：card domain	Not recorded	SO4 SULFATE ION × 7 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；13% PEG 3000, 0.2M ammonium sulfate, 0.1M MES (pH5.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.226
5JUY Active human apoptosome with procaspase-9 Deposited 2016-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–1248（1248 aa） Chain B 1–1248（1248 aa） Chain C 1–1248（1248 aa） Chain D 1–1248（1248 aa） Chain E 1–1248（1248 aa） Chain F 1–1248（1248 aa） Chain G 1–1248（1248 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 HEC HEME C × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Buffer A cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
5WVC Structure of the CARD-CARD disk Deposited 2016-12-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–95（95 aa） Fragment：UNP RESIDUES 1-95 Chain C 1–95（95 aa） Fragment：UNP RESIDUES 1-95 Chain E 1–95（95 aa） Fragment：UNP RESIDUES 1-95	Not recorded	IOD IODIDE ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M NH4I, 20% PEG 3350	Resolution 2.99 Å R-free 0.228
5WVE Apaf-1-Caspase-9 holoenzyme Deposited 2016-12-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric	Chain A 1–1248（1248 aa） Chain C 1–1248（1248 aa） Chain E 1–1248（1248 aa） Chain G 1–1248（1248 aa） Chain I 1–1248（1248 aa） Chain K 1–1248（1248 aa） Chain M 1–1248（1248 aa） Chain O 1–102（102 aa） Fragment：CARD domain, UNP residues 1-102 Chain P 1–102（102 aa） Fragment：CARD domain, UNP residues 1-102 Chain Q 1–102（102 aa） Fragment：CARD domain, UNP residues 1-102 Chain R 1–102（102 aa） Fragment：CARD domain, UNP residues 1-102 Chain W 1–102（102 aa） Fragment：CARD domain, UNP residues 1-102 Chain X 1–102（102 aa） Fragment：CARD domain, UNP residues 1-102	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
8XQK The Crystal Structure of Apaf from Biortus. Deposited 2024-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–97（97 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.6M Na/KPO4 pH6.5	Resolution 2.85 Å R-free 0.283
8XQK The Crystal Structure of Apaf from Biortus. Deposited 2024-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–97（97 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.6M Na/KPO4 pH6.5	Resolution 2.85 Å R-free 0.283
8XQK The Crystal Structure of Apaf from Biortus. Deposited 2024-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–97（97 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.6M Na/KPO4 pH6.5	Resolution 2.85 Å R-free 0.283
8XQK The Crystal Structure of Apaf from Biortus. Deposited 2024-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–97（97 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.6M Na/KPO4 pH6.5	Resolution 2.85 Å R-free 0.283

13 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	APAF_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–95； UniProt 1–95

PROCASPASE 9

Homo sapiens

UniProt P55211

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain P； UniProt 1–96	Fragment：PRODOMAIN	APOPTOTIC PROTEASE ACTIVATING FACTOR 1 × 1 （O14727）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.50 Å R-free 0.299

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3YGS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NW9 STRUCTURE OF CASPASE-9 IN AN INHIBITORY COMPLEX WITH XIAP-BIR3 Deposited 2003-02-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 140–416（277 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Tris, potassium phosphate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.235
2AR9 Crystal structure of a dimeric caspase-9 Deposited 2005-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 140–416（277 aa） Fragment：residues 140-416 Chain B 140–416（277 aa） Fragment：residues 140-416	Mutation：C287S, G402C, C403I, F404V, N405S, F406M Mutation：C287S, G402C, C403I, F404V, N405S, F406M	MLT D-MALATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；PEG5000 monomethylether, MES, tacsimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.80 Å R-free 0.288
2AR9 Crystal structure of a dimeric caspase-9 Deposited 2005-08-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 140–416（277 aa） Fragment：residues 140-416 Chain D 140–416（277 aa） Fragment：residues 140-416	Mutation：C287S, G402C, C403I, F404V, N405S, F406M Mutation：C287S, G402C, C403I, F404V, N405S, F406M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；PEG5000 monomethylether, MES, tacsimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.80 Å R-free 0.288
3D9T CIAP1-BIR3 in complex with N-terminal peptide from Caspase-9 (ATPFQE) Deposited 2008-05-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 316–321（6 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.1M NA FORMATE,10% GLYCEROL,1.5MM PEPTIDE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.205
3D9T CIAP1-BIR3 in complex with N-terminal peptide from Caspase-9 (ATPFQE) Deposited 2008-05-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 316–321（6 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.1M NA FORMATE,10% GLYCEROL,1.5MM PEPTIDE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.205
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
4RHW Crystal structure of Apaf-1 CARD and caspase-9 CARD complex Deposited 2014-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–100（100 aa） Fragment：card domain Chain F 1–100（100 aa） Fragment：card domain	Not recorded	SO4 SULFATE ION × 7 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；13% PEG 3000, 0.2M ammonium sulfate, 0.1M MES (pH5.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.226
5JUY Active human apoptosome with procaspase-9 Deposited 2016-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain O 1–95（95 aa） Fragment：N-terminal caspase recognition domain Chain P 1–95（95 aa） Fragment：N-terminal caspase recognition domain Chain Q 1–95（95 aa） Fragment：N-terminal caspase recognition domain Chain R 1–95（95 aa） Fragment：N-terminal caspase recognition domain	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 HEC HEME C × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Buffer A cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
9R44 Crystal structure of human caspase-9 CARD Deposited 2025-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–99（99 aa） Chain E 1–99（99 aa） Chain H 1–99（99 aa） Chain L 1–99（99 aa）	Not recorded	SO4 SULFATE ION × 18 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.5 M Lithium sulfate, 0.1 M Sodium HEPES, and pH 7.5 Protein concentration: 15 mg/ml Buffer in: 20 mM Hepes, 50 mM NaCl, 2 mM TCEP, and pH 7.5	Resolution 2.46 Å R-free 0.265

7 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CASP9_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 2–97； UniProt 1–96

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ygs
Deposition date deposition_date	1999-05-08
Structure title title	APAF-1 CARD IN COMPLEX WITH PRODOMAIN OF PROCASPASE-9
Keywords keywords	APOPTOSIS, CASPASE ACTIVATION, CASPASE RECRUITMENT, RECOGNITION COMPLEX; APOPTOSIS
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.64 Å
Radius of gyration Rg (electron density) rg_electron	17.77 Å
Forward intensity I(0) i0	9543450.00
Molecular weight molecular_weight	22202.0 kDa
Excluded volume excluded_volume	27515 Å³
Envelope volume envelope_volume	31433 Å³
Hydration-shell volume shell_volume	15357 Å³
Envelope diameter envelope_diameter	59.8 Å
Shell Rg shell_rg	23.00 Å
Envelope Rg envelope_rg	17.98 Å
Shape Rg shape_rg	17.77 Å
Total Rg total_rg	18.55 Å
Total atoms total_atoms	1553
Residues n_residues	192
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	61.6 Å
Rg (real space) rg_real	18.64 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	9.5430e+06
I(0) uncertainty (real space) i0_real_error	1.1640e+05
Rg (reciprocal space) rg_reciprocal	18.64 Å
I(0) (reciprocal space) i0_reciprocal	9543000.0000
Solution quality estimate total_estimate	0.8749
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.364
Kurtosis Kurtosis kurtosis	-0.356
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2326000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.795; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.992

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	APOPTOTIC PROTEASE ACTIVATING FACTOR 1
Molecular weight formula_weight	10925.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	1726

MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	PROCASPASE 9
Molecular weight formula_weight	11312.9 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

SMDEADRRLLRRCRLRLVEELQVDQLWDVLLSRELFRPHMIEDIQRAGSGSRRDQARQLIIDLETRGSQALPLFISCLEDTGQDMLASFLRTNRQAG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	173

▼

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3ygsc_
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.3 — Caspase recruitment domain, CARD

Domain ID domain_id	d3ygsp1
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.3 — Caspase recruitment domain, CARD

Domain ID domain_id	d3ygsp2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	3ygsC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	3ygsP00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

▶

8. Citations (1)

▶

Unit-cell length a length_a	92.500 Å
Unit-cell length b length_b	92.500 Å
Unit-cell length c length_c	136.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.2240
R_free r_free	0.2990

fit	/app/data/saxs_computation/yg/3ygs/3ygs.fit
pddf	/app/data/pr_computation/yg/3ygs/3ygs.pr.out
profile	/app/data/saxs_computation/yg/3ygs/3ygs.dat

APAF-1 CARD IN COMPLEX WITH PRODOMAIN OF PROCASPASE-9

1. Protein Identity and Related Structures Protein Identity & Related Structures

APOPTOTIC PROTEASE ACTIVATING FACTOR 1

State in the Current Structure

Other States of the Same Protein in the Database

PROCASPASE 9

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)